Biomass feedstock pretreatment with ionic liquids (ILs) reduces recalcitrance of lignocellulose to degradation. However, ILs are often toxic to microorganisms used subsequently for saccharification and fermentation and the low levels of IL that can remain after pretreatment inhibit the growth of organism used in saccharification and/or fermentation reactions. There is therefore a need to improve IL tolerance of such organisms. This invention addresses this need.